[gmx-users] Thermodynamic integration
mark.j.abraham at gmail.com
Mon Apr 18 12:53:45 CEST 2016
Also you might consider pmx
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4365728/ for such topology
generation. There is further work in the pipeline, so do get in touch with
Bert if there's something of interest.
On Mon, Apr 18, 2016 at 11:56 AM Nash, Anthony <a.nash at ucl.ac.uk> wrote:
> From the site, “..or the free energy of a mutation of a side chain.”
> I think this is what I am after. Many thanks for the link.
> On 18/04/2016 10:42, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
> behalf of Hannes Loeffler"
> <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of
> Hannes.Loeffler at stfc.ac.uk> wrote:
> >A good starting point is http://www.alchemistry.org/ which has quite a
> >lot of detail on relative alchemical free energy simulations (not only
> >On Mon, 18 Apr 2016 09:27:02 +0000
> >"Nash, Anthony" <a.nash at ucl.ac.uk> wrote:
> >> Hi all,
> >> I¹m looking for a guide on performing TI between a protein in its
> >> crystal periodicity with a particular residue (state A), to the same
> >> system but with a different residue (state B).
> >> I¹m currently using
> >> _energy/01_theory.html as a guide, however this is more, if I
> >> understand having read through it, on the presence-to-absence of
> >> methane in a water solvent rather than a replacement with something
> >> else.
> >> I haven¹t had too much luck googling and I¹m looking piecemeal
> >> through the manual with little success.
> >> Thanks
> >> Anthony
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